2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/
26 package org.forester.io.parsers.phyloxml.data;
28 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
29 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
30 import org.forester.io.parsers.phyloxml.XmlElement;
31 import org.forester.phylogeny.data.PhylogenyData;
32 import org.forester.phylogeny.data.Property;
33 import org.forester.phylogeny.data.Property.AppliesTo;
34 import org.forester.util.ForesterUtil;
36 public class PropertyParser implements PhylogenyDataPhyloXmlParser {
38 private static final PhylogenyDataPhyloXmlParser _instance;
41 _instance = new PropertyParser();
43 catch ( final Throwable e ) {
44 throw new RuntimeException( e.getMessage() );
48 private PropertyParser() {
52 public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException {
57 String applies_to_str = "";
59 if ( element.isHasAttribute( PhyloXmlMapping.PROPERTY_REF ) ) {
60 ref = element.getAttribute( PhyloXmlMapping.PROPERTY_REF );
62 if ( element.isHasAttribute( PhyloXmlMapping.PROPERTY_UNIT ) ) {
63 unit = element.getAttribute( PhyloXmlMapping.PROPERTY_UNIT );
65 if ( element.isHasAttribute( PhyloXmlMapping.PROPERTY_DATATYPE ) ) {
66 datatype = element.getAttribute( PhyloXmlMapping.PROPERTY_DATATYPE );
68 if ( element.isHasAttribute( PhyloXmlMapping.PROPERTY_APPLIES_TO ) ) {
69 applies_to_str = element.getAttribute( PhyloXmlMapping.PROPERTY_APPLIES_TO );
71 if ( element.isHasAttribute( PhyloXmlMapping.ID_REF ) ) {
72 id_ref = element.getAttribute( PhyloXmlMapping.ID_REF );
74 if ( !ForesterUtil.isEmpty( element.getValueAsString() ) ) {
75 value = element.getValueAsString();
77 AppliesTo applies_to = AppliesTo.OTHER;
78 if ( applies_to_str.equals( AppliesTo.NODE.toString() ) ) {
79 applies_to = AppliesTo.NODE;
81 else if ( applies_to_str.equals( AppliesTo.PARENT_BRANCH.toString() ) ) {
82 applies_to = AppliesTo.PARENT_BRANCH;
84 else if ( applies_to_str.equals( AppliesTo.CLADE.toString() ) ) {
85 applies_to = AppliesTo.CLADE;
87 else if ( applies_to_str.equals( AppliesTo.ANNOTATION.toString() ) ) {
88 applies_to = AppliesTo.ANNOTATION;
90 else if ( applies_to_str.equals( AppliesTo.PHYLOGENY.toString() ) ) {
91 applies_to = AppliesTo.PHYLOGENY;
93 return new Property( ref, value, unit, datatype, applies_to, id_ref );
96 public static PhylogenyDataPhyloXmlParser getInstance() {